This page contains the results of CoNGA analyses.
Results in tables may have been filtered to reduce redundancy,
focus on the most important columns, and
limit length; full tables should exist as OUTFILE_PREFIX*.tsv files.
Here we are assessing overall graph-vs-graph correlation by looking at
the shared edges between TCR and GEX neighbor graphs and comparing
that observed number to the number we would expect if the graphs were
completely uncorrelated. Our null model for uncorrelated graphs is to
take the vertices of one graph and randomly renumber them (permute their
labels). We compare the observed overlap to that expected under this null
model by computing a Z-score, either by permuting one of the graph's
vertices many times to get a mean and standard deviation of the overlap
distribution, or, for large graphs where this is time consuming,
by using a regression model for the
standard deviation. The different rows of this table correspond to the
different graph-graph comparisons that we make in the conga graph-vs-graph
analysis: we compare K-nearest-neighbor graphs for GEX and TCR at different
K values ("nbr_frac" aka neighbor-fraction, which reports K as a fraction
of the total number of clonotypes) to each other and to GEX and TCR "cluster"
graphs in which each clonotype is connected to all the other clonotypes with
the same (GEX or TCR) cluster assignment. For two K values (the default),
this gives 2*3=6 comparisons: GEX KNN graph vs TCR KNN graph, GEX cluster
graph vs TCR KNN graph, and GEX KNN graph vs TCR cluster graph, for each of the
two K values (aka nbr_fracs).
The column to look at is *overlap_zscore*. Higher values indicate more
significant GEX/TCR covariation, with "interesting" levels starting around
zscores of 3-5.
Columns in more detail:
graph_overlap_type: KNN ("nbr") or cluster versus KNN ("nbr") or cluster
nbr_frac: the K value for the KNN graph, as a fraction of total clonotypes
overlap: the observed overlap (number of shared edges) between GEX and TCR
graphs
expected_overlap: the expected overlap under a shuffled null model.
overlap_zscore: a Z-score for the observed overlap computed by subtracting
the expected overlap and dividing by the standard deviation estimated from
shuffling.
overlap
expected_overlap
overlap_mean
overlap_sdev
overlap_zscore
overlap_zscore_fitted
overlap_zscore_source
nodes
calculation_time
calculation_time_fitted
gex_edges
tcr_edges
gex_indegree_variance
gex_indegree_skewness
gex_indegree_kurtosis
tcr_indegree_variance
tcr_indegree_skewness
tcr_indegree_kurtosis
indegree_correlation_R
indegree_correlation_P
nbr_frac
graph_overlap_type
145
100.097943
97.95
10.238530
4.595386
5.204296
shuffling
1022
0.078408
0.006556
10220
10220
1.151087
2.610250
11.803733
0.328188
1.266386
2.340896
-0.019298
0.537748
0.01
gex_nbr_vs_tcr_nbr
1325
1116.826641
1117.38
34.805109
5.965216
5.569579
shuffling
1022
0.690925
0.081416
10220
114028
1.151087
2.610250
11.803733
0.148074
-0.064423
-1.198669
-0.025537
0.414783
0.01
gex_nbr_vs_tcr_cluster
2378
1870.029383
1869.08
45.993191
11.065116
12.114015
shuffling
1022
1.355610
0.139480
190930
10220
0.200400
-0.134656
-0.890258
0.328188
1.266386
2.340896
0.026277
0.401376
0.01
gex_cluster_vs_tcr_nbr
11400
10414.190010
10428.41
191.350521
5.077540
5.318187
shuffling
1022
1.105426
0.687331
104244
104244
0.838358
1.251051
1.457115
0.255108
1.689155
4.650548
0.025090
0.422995
0.10
gex_nbr_vs_tcr_nbr
12613
11391.631734
11383.36
167.445724
7.343514
7.108298
shuffling
1022
1.146984
0.754843
104244
114028
0.838358
1.251051
1.457115
0.148074
-0.064423
-1.198669
0.008925
0.775658
0.10
gex_nbr_vs_tcr_cluster
21086
19074.299706
19093.15
186.260698
10.699251
10.265160
shuffling
1022
1.850863
1.293179
190930
104244
0.200400
-0.134656
-0.890258
0.255108
1.689155
4.650548
0.027809
0.374479
0.10
gex_cluster_vs_tcr_nbr
graph_vs_graph
Graph vs graph analysis looks for correlation between GEX and TCR space
by finding statistically significant overlap between two similarity graphs,
one defined by GEX similarity and one by TCR sequence similarity.
Overlap is defined one node (clonotype) at a time by looking for overlap
between that node's neighbors in the GEX graph and its neighbors in the
TCR graph. The null model is that the two neighbor sets are chosen
independently at random.
CoNGA looks at two kinds of graphs: K nearest neighbor (KNN) graphs, where
K = neighborhood size is specified as a fraction of the number of
clonotypes (defaults for K are 0.01 and 0.1), and cluster graphs, where
each clonotype is connected to all the other clonotypes in the same
(GEX or TCR) cluster. Overlaps are computed 3 ways (GEX KNN vs TCR KNN,
GEX KNN vs TCR cluster, and GEX cluster vs TCR KNN), for each of the
K values (called nbr_fracs short for neighbor fractions).
Columns (depend slightly on whether hit is KNN v KNN or KNN v cluster):
conga_score = P value for GEX/TCR overlap * number of clonotypes
mait_fraction = fraction of the overlap made up of 'invariant' T cells
num_neighbors* = size of neighborhood (K)
cluster_size = size of cluster (for KNN v cluster graph overlaps)
clone_index = 0-index of clonotype in adata object
conga_score
num_neighbors_gex
num_neighbors_tcr
overlap
overlap_corrected
mait_fraction
clone_index
nbr_frac
graph_overlap_type
cluster_size
gex_cluster
tcr_cluster
va
ja
cdr3a
vb
jb
cdr3b
1.362550e-08
NaN
10.0
10
9
1.000000
27
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQGPGGASVLTF
1.261473e-07
NaN
10.0
10
8
1.000000
35
0.01
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV24-1*01
TRBJ2-6*01
CATSSDSSGASVLTF
1.261473e-07
NaN
10.0
10
8
1.000000
33
0.01
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-2*01
TRBJ2-6*01
CASSVDSDSGASVLTF
2.060094e-07
NaN
10.0
10
8
1.000000
31
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDQNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQDQEGTGASVLTF
1.572245e-06
NaN
10.0
9
8
1.000000
28
0.01
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQVPGTGASVLTF
1.996482e-06
NaN
10.0
9
8
1.000000
22
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAALDSNYQLIW
TRBV4-3*01
TRBJ1-2*01
CASSQGGAPDYDYTF
1.996482e-06
NaN
10.0
9
8
1.000000
41
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVWDSNYQLIW
TRBV4-3*01
TRBJ2-2*01
CASSQDWGEPGAQLFF
6.715313e-06
NaN
10.0
8
8
1.000000
36
0.01
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-1*01
TRBJ2-2*01
CASSVRGETAQLFF
1.763080e-05
NaN
10.0
9
7
1.000000
38
0.01
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-2*01
TRBJ2-6*01
CASSEAASGASVLTF
2.688248e-05
NaN
10.0
9
7
1.000000
23
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAAMDSNYQLIW
TRBV4-2*01
TRBJ2-2*01
CASSQAMGEHGAQLFF
2.688248e-05
NaN
10.0
9
7
1.000000
32
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDRDYQLIW
TRBV19*01
TRBJ2-6*01
CASSSGNSGASVLTF
6.491113e-05
NaN
102.0
23
21
0.652174
34
0.10
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-3*01
TRBJ1-5*01
CASSEGGEVNQPQYF
6.491113e-05
NaN
102.0
23
21
0.652174
38
0.10
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-2*01
TRBJ2-6*01
CASSEAASGASVLTF
1.042252e-04
NaN
10.0
8
7
1.000000
29
0.01
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQDIGGSSGASVLTF
1.599297e-04
NaN
102.0
26
20
0.730769
32
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDRDYQLIW
TRBV19*01
TRBJ2-6*01
CASSSGNSGASVLTF
3.012966e-04
NaN
10.0
7
7
1.000000
34
0.01
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-3*01
TRBJ1-5*01
CASSEGGEVNQPQYF
3.019490e-04
NaN
10.0
9
6
1.000000
30
0.01
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV6-3*01
TRBJ2-6*01
CASNMRHSGASVLTF
3.611443e-04
NaN
102.0
22
20
0.681818
33
0.10
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-2*01
TRBJ2-6*01
CASSVDSDSGASVLTF
3.621572e-04
NaN
10.0
9
6
1.000000
26
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAPRDSNYQLIW
TRBV6-1*01
TRBJ2-6*01
CASSEGYSGASVLTF
3.621572e-04
NaN
10.0
9
6
1.000000
25
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAPMDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSWDNSGASVLTF
3.621572e-04
NaN
10.0
9
6
1.000000
39
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSDGGESGASVLTF
6.274256e-04
NaN
102.0
38
38
0.000000
567
0.10
gex_cluster_vs_tcr_nbr
182.0
2
6
TRAV27*01
TRAJ53*01
CAGAYSGSSNYKLTF
TRBV20-1*01
TRBJ2-2*01
CSARRRTNTAQLFF
8.686281e-04
NaN
102.0
25
19
0.760000
39
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSDGGESGASVLTF
8.686281e-04
NaN
102.0
25
19
0.760000
25
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAPMDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSWDNSGASVLTF
8.686281e-04
NaN
102.0
25
19
0.760000
27
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQGPGGASVLTF
1.163187e-03
10.0
NaN
6
6
1.000000
36
0.01
gex_nbr_vs_tcr_cluster
46.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-1*01
TRBJ2-2*01
CASSVRGETAQLFF
1.847839e-03
NaN
102.0
21
19
0.714286
35
0.10
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV24-1*01
TRBJ2-6*01
CATSSDSSGASVLTF
1.980417e-03
102.0
NaN
26
26
0.000000
634
0.10
gex_nbr_vs_tcr_cluster
104.0
5
3
TRAV38-1*01
TRAJ43*01
CAFMKENNDIRF
TRBV9*01
TRBJ1-3*01
CASSLGQESGNTVYF
4.247237e-03
102.0
NaN
20
20
0.000000
218
0.10
gex_nbr_vs_tcr_cluster
70.0
2
6
TRAV13-1*01
TRAJ47*01
CAAIFYGNKLIF
TRBV20-1*01
TRBJ1-3*01
CSALNGGSGNTVYF
4.329108e-03
NaN
102.0
24
18
0.791667
18
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ20*01
CAVRDRDYKLSF
TRBV4-3*01
TRBJ2-4*01
CASSQDLGGSDTQYF
4.329108e-03
NaN
102.0
24
18
0.791667
26
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAPRDSNYQLIW
TRBV6-1*01
TRBJ2-6*01
CASSEGYSGASVLTF
4.552048e-03
102.0
NaN
21
15
0.904762
24
0.10
gex_nbr_vs_tcr_cluster
51.0
4
8
TRAV1-2*01
TRAJ33*01
CAFMDSNYQLIW
TRBV6-1*01
TRBJ2-3*01
CASSGTGDTDPQYF
4.715481e-03
NaN
10.0
7
6
1.000000
18
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ20*01
CAVRDRDYKLSF
TRBV4-3*01
TRBJ2-4*01
CASSQDLGGSDTQYF
6.117287e-03
NaN
102.0
22
18
0.772727
30
0.10
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV6-3*01
TRBJ2-6*01
CASNMRHSGASVLTF
6.117287e-03
NaN
102.0
22
18
0.772727
29
0.10
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQDIGGSSGASVLTF
8.682594e-03
NaN
102.0
20
18
0.750000
36
0.10
gex_cluster_vs_tcr_nbr
64.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-1*01
TRBJ2-2*01
CASSVRGETAQLFF
1.067573e-02
10.0
NaN
7
5
0.857143
27
0.01
gex_nbr_vs_tcr_cluster
51.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQGPGGASVLTF
1.122430e-02
102.0
NaN
32
32
0.000000
906
0.10
gex_nbr_vs_tcr_cluster
156.0
0
1
TRAV8-3*01
TRAJ8*01
CAVSERNTGFQKLVF
TRBV23-1*01
TRBJ2-7*01
CASSPQGEYEQYF
1.976548e-02
NaN
102.0
23
17
0.826087
41
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVWDSNYQLIW
TRBV4-3*01
TRBJ2-2*01
CASSQDWGEPGAQLFF
1.976548e-02
NaN
102.0
23
17
0.826087
23
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAAMDSNYQLIW
TRBV4-2*01
TRBJ2-2*01
CASSQAMGEHGAQLFF
1.976548e-02
NaN
102.0
23
17
0.826087
31
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVRDQNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQDQEGTGASVLTF
1.976548e-02
NaN
102.0
23
17
0.826087
40
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVTDSNYQLIW
TRBV6-1*01
TRBJ1-2*01
CASSDWDSNYDYTF
2.563956e-02
10.0
NaN
6
5
1.000000
23
0.01
gex_nbr_vs_tcr_cluster
51.0
4
8
TRAV1-2*01
TRAJ33*01
CAAMDSNYQLIW
TRBV4-2*01
TRBJ2-2*01
CASSQAMGEHGAQLFF
2.713711e-02
NaN
102.0
21
17
0.809524
28
0.10
gex_cluster_vs_tcr_nbr
66.0
4
8
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQVPGTGASVLTF
3.553112e-02
NaN
102.0
48
48
0.000000
825
0.10
gex_cluster_vs_tcr_nbr
296.0
0
1
TRAV8-2*01
TRAJ29*01
CAVNVSGNRALVF
TRBV9*01
TRBJ2-1*01
CASSYRGWGDNEQFF
4.789739e-02
NaN
10.0
7
5
1.000000
40
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAVTDSNYQLIW
TRBV6-1*01
TRBJ1-2*01
CASSDWDSNYDYTF
4.789739e-02
NaN
10.0
7
5
1.000000
24
0.01
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ33*01
CAFMDSNYQLIW
TRBV6-1*01
TRBJ2-3*01
CASSGTGDTDPQYF
5.452475e-02
10.0
NaN
5
5
1.000000
24
0.01
gex_nbr_vs_tcr_cluster
51.0
4
8
TRAV1-2*01
TRAJ33*01
CAFMDSNYQLIW
TRBV6-1*01
TRBJ2-3*01
CASSGTGDTDPQYF
5.815087e-02
102.0
102.0
23
23
0.000000
368
0.10
gex_nbr_vs_tcr_nbr
NaN
6
3
TRAV19*01
TRAJ43*01
CALIQYNNNDIRF
TRBV6-1*01
TRBJ2-3*01
CASSDFGLGQGYPQYF
6.007283e-02
NaN
102.0
20
17
0.700000
17
0.10
gex_cluster_vs_tcr_nbr
68.0
4
8
TRAV1-2*01
TRAJ12*01
CAVRDPGDGGYKLIF
TRBV7-2*01
TRBJ2-7*01
CASSPSWSGSYAEQYF
Omitted 70 lines
graph_vs_graph_logos
This figure summarizes the results of a CoNGA analysis that produces
scores (CoNGA) and clusters. At the top are six
2D UMAP projections of clonotypes in the dataset based on GEX similarity
(top left three panels) and TCR similarity (top right three panels),
colored from left to right by GEX cluster assignment;
CoNGA score; joint GEX:TCR cluster assignment for
clonotypes with significant CoNGA scores,
using a bicolored disk whose left half indicates GEX cluster and whose right
half indicates TCR cluster; TCR cluster; CoNGA; GEX:TCR cluster
assignments for CoNGA hits, as in the third panel.
Below are two rows of GEX landscape plots colored by (first row, left)
expression of selected marker genes, (second row, left) Z-score normalized and
GEX-neighborhood averaged expression of the same marker genes, and
(both rows, right) TCR sequence features (see CoNGA manuscript Table S3 for
TCR feature descriptions).
GEX and TCR sequence features of CoNGA hits in clusters with
5 or more hits are summarized by a series
of logo-style visualizations, from left to right:
differentially expressed genes (DEGs); TCR sequence logos showing the V and
J gene usage and CDR3 sequences for the TCR alpha and beta chains; biased
TCR sequence scores, with red indicating elevated scores and blue indicating
decreased scores relative to the rest of the dataset (see CoNGA manuscript
Table S3 for score definitions); GEX 'logos' for each cluster
consisting of a panel of marker genes shown with red disks colored by
mean expression and sized according to the fraction of cells expressing
the gene (gene names are given above).
DEG and TCRseq sequence logos are scaled
by the adjusted P value of the associations, with full logo height requiring
a top adjusted P value below 10-6. DEGs with fold-change less than 2 are shown
in gray. Each cluster is indicated by a bicolored disk colored according to
GEX cluster (left half) and TCR cluster (right half). The two numbers above
each disk show the number of hits within the cluster (on the left) and
the total number of cells in those clonotypes (on the right). The dendrogram
at the left shows similarity relationships among the clusters based on
connections in the GEX and TCR neighbor graphs.
The choice of which marker genes to use for the GEX umap panels and for the
cluster GEX logos can be configured using run_conga.py command line flags
or arguments to the conga.plotting.make_logo_plots function.
Image source: Cobain_GIC_Final2_graph_vs_graph_logos.png
tcr_clumping
This table stores the results of the TCR "clumping"
analysis, which looks for neighborhoods in TCR space with more TCRs than
expected by chance under a simple null model of VDJ rearrangement.
For each TCR in the dataset, we count how many TCRs are within a set of
fixed TCRdist radii (defaults: 24,48,72,96), and compare that number
to the expected number given the size of the dataset using the poisson
model. Inspired by the ALICE and TCRnet methods.
Columns:
clump_type='global' unless we are optionally looking for TCR clumps within
the individual GEX clusters
num_nbrs = neighborhood size (number of other TCRs with TCRdist
clump_type
clone_index
nbr_radius
pvalue_adj
num_nbrs
expected_num_nbrs
raw_count
va
ja
cdr3a
vb
jb
cdr3b
clonotype_fdr_value
clumping_group
clusters_gex
clusters_tcr
global
25
96
1.022558e-13
7
1.438834e-02
35231.0
TRAV1-2*01
TRAJ33*01
CAPMDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSWDNSGASVLTF
7.719460e-14
1
4
8
global
26
96
1.758442e-13
9
6.338940e-02
155214.0
TRAV1-2*01
TRAJ33*01
CAPRDSNYQLIW
TRBV6-1*01
TRBJ2-6*01
CASSEGYSGASVLTF
7.719460e-14
1
4
8
global
39
96
2.315838e-13
7
1.617427e-02
39604.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSDGGESGASVLTF
7.719460e-14
1
4
8
global
697
24
4.073907e-12
4
3.932892e-04
963.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CAIAGTNYGEQFF
1.018477e-12
2
3
5
global
696
24
5.878051e-11
4
7.665668e-04
1877.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
692
24
5.878051e-11
4
7.665668e-04
1877.0
TRAV4*01
TRAJ33*01
CLGGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
32
96
7.823386e-10
5
7.460243e-03
18267.0
TRAV1-2*01
TRAJ33*01
CAVRDRDYQLIW
TRBV19*01
TRBJ2-6*01
CASSSGNSGASVLTF
1.117627e-10
1
4
8
global
697
48
2.194520e-08
4
3.371342e-03
8255.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CAIAGTNYGEQFF
1.018477e-12
2
3
5
global
698
24
3.306834e-08
3
3.648020e-04
895.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSATNYGEQFF
3.674260e-09
2
1
5
global
696
48
2.120609e-07
4
5.947121e-03
14562.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
692
48
2.120609e-07
4
5.947121e-03
14562.0
TRAV4*01
TRAJ33*01
CLGGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
699
24
3.049340e-07
3
7.650652e-04
1877.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
2.541116e-08
2
3
5
global
35
96
1.122888e-05
4
1.607515e-02
39555.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV24-1*01
TRBJ2-6*01
CATSSDSSGASVLTF
8.637600e-07
1
4
8
global
30
96
1.485439e-05
4
1.724393e-02
42306.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV6-3*01
TRBJ2-6*01
CASNMRHSGASVLTF
1.061028e-06
1
4
8
global
38
96
1.704181e-05
5
5.544312e-02
136425.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-2*01
TRBJ2-6*01
CASSEAASGASVLTF
1.136121e-06
1
4
8
global
698
48
2.193538e-05
3
3.183764e-03
7811.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSATNYGEQFF
3.674260e-09
2
1
5
global
697
72
4.739480e-05
4
2.307337e-02
56497.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CAIAGTNYGEQFF
1.018477e-12
2
3
5
global
699
48
1.418379e-04
3
5.935471e-03
14562.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
2.541116e-08
2
3
5
global
696
72
3.119086e-04
4
3.705944e-02
90743.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
692
72
3.119086e-04
4
3.705944e-02
90743.0
TRAV4*01
TRAJ33*01
CLGGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
27
96
3.159402e-04
4
3.717951e-02
91037.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQGPGGASVLTF
1.504477e-05
1
4
8
global
26
72
3.766370e-04
3
8.223951e-03
20137.0
TRAV1-2*01
TRAJ33*01
CAPRDSNYQLIW
TRBV6-1*01
TRBJ2-6*01
CASSEGYSGASVLTF
7.719460e-14
1
4
8
global
28
96
2.034865e-03
3
1.445309e-02
35459.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQVPGTGASVLTF
8.847240e-05
1
4
8
global
621
24
3.339077e-03
1
8.168000e-07
2.0
TRAV35*01
TRAJ58*01
CAGQRQTGGSRLTF
TRBV14*01
TRBJ1-2*01
CASSQGYDYTF
1.335631e-04
6
0
4
global
620
24
3.339077e-03
1
8.168000e-07
2.0
TRAV35*01
TRAJ58*01
CAGQRQTGGSRLTF
TRBV14*01
TRBJ1-2*01
CASSQGYDYTF
1.335631e-04
6
0
4
global
28
72
7.148618e-03
2
1.871292e-03
4591.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQVPGTGASVLTF
8.847240e-05
1
4
8
global
698
72
9.480741e-03
3
2.419840e-02
59368.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSATNYGEQFF
3.674260e-09
2
1
5
global
39
72
1.221638e-02
2
2.446724e-03
5991.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-1*01
TRBJ2-6*01
CASSDGGESGASVLTF
7.719460e-14
1
4
8
global
529
24
2.003442e-02
1
4.900800e-06
12.0
TRAV27*01
TRAJ17*01
CAGEGVASNKLTF
TRBV21-1*01
TRBJ1-5*01
CASSSGQGDQPQYF
6.678140e-04
5
1
4
global
268
24
2.003442e-02
1
4.900800e-06
12.0
TRAV17*01
TRAJ27*01
CATDANADKLTF
TRBV19*01
TRBJ2-4*01
CASGQGGQNTQYF
6.678140e-04
4
3
2
global
697
96
2.474122e-02
4
1.122700e-01
274902.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CAIAGTNYGEQFF
1.018477e-12
2
3
5
global
269
24
2.838207e-02
1
6.942800e-06
17.0
TRAV17*01
TRAJ27*01
CATDTNADKLTF
TRBV19*01
TRBJ2-4*01
CASGQGGQNTQYF
8.869396e-04
4
3
2
global
699
72
3.353245e-02
3
3.698685e-02
90743.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
2.541116e-08
2
3
5
global
27
72
3.760043e-02
2
4.295143e-03
10517.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQGPGGASVLTF
1.504477e-05
1
4
8
global
70
24
5.008587e-02
1
1.225200e-05
30.0
TRAV12-1*01
TRAJ36*01
CAVRTGVNNLFF
TRBV23-1*01
TRBJ2-7*01
CASSQTGTGSYEQYF
1.431025e-03
3
6
0
global
31
96
8.366437e-02
2
6.411472e-03
15699.0
TRAV1-2*01
TRAJ33*01
CAVRDQNYQLIW
TRBV4-2*01
TRBJ2-6*01
CASSQDQEGTGASVLTF
2.324010e-03
1
4
8
global
71
24
8.681512e-02
1
2.123680e-05
52.0
TRAV12-1*01
TRAJ36*01
CAVRTGVNNLFF
TRBV23-1*01
TRBJ2-7*01
CASSSTGTGSYEQYF
2.346355e-03
3
6
0
global
37
96
9.273157e-02
3
5.211227e-02
128229.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-1*01
TRBJ2-6*01
CASSEARTGASVLTF
2.440305e-03
1
2
8
global
528
24
9.683213e-02
1
2.368720e-05
58.0
TRAV27*01
TRAJ17*01
CAGEEVASNKLTF
TRBV21-1*01
TRBJ1-5*01
CASSKGQGDQPQYF
2.482875e-03
5
3
4
global
621
48
1.101881e-01
1
2.695440e-05
66.0
TRAV35*01
TRAJ58*01
CAGQRQTGGSRLTF
TRBV14*01
TRBJ1-2*01
CASSQGYDYTF
1.335631e-04
6
0
4
global
620
48
1.101881e-01
1
2.695440e-05
66.0
TRAV35*01
TRAJ58*01
CAGQRQTGGSRLTF
TRBV14*01
TRBJ1-2*01
CASSQGYDYTF
1.335631e-04
6
0
4
global
38
72
1.197466e-01
2
7.673645e-03
18882.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV6-2*01
TRBJ2-6*01
CASSEAASGASVLTF
1.136121e-06
1
4
8
global
696
96
1.260330e-01
4
1.706377e-01
417820.0
TRAV4*01
TRAJ33*01
CLVGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
692
96
1.260330e-01
4
1.706377e-01
417820.0
TRAV4*01
TRAJ33*01
CLGGDSNYQLIW
TRBV10-1*01
TRBJ2-1*01
CASSGTNYGEQFF
9.796751e-12
2
3
5
global
33
96
2.149163e-01
2
1.028924e-02
25318.0
TRAV1-2*01
TRAJ33*01
CAVRDSNYQLIW
TRBV10-2*01
TRBJ2-6*01
CASSVDSDSGASVLTF
4.775917e-03
1
4
8
global
23
96
2.709446e-01
2
1.155772e-02
28300.0
TRAV1-2*01
TRAJ33*01
CAAMDSNYQLIW
TRBV4-2*01
TRBJ2-2*01
CASSQAMGEHGAQLFF
5.890101e-03
1
4
8
global
29
96
2.957849e-01
2
1.207800e-02
29632.0
TRAV1-2*01
TRAJ33*01
CAVMDSNYQLIW
TRBV4-3*01
TRBJ2-6*01
CASSQDIGGSSGASVLTF
6.293296e-03
1
4
8
global
529
48
5.091777e-01
1
1.245620e-04
305.0
TRAV27*01
TRAJ17*01
CAGEGVASNKLTF
TRBV21-1*01
TRBJ1-5*01
CASSSGQGDQPQYF
6.678140e-04
5
1
4
global
268
48
6.160135e-01
1
1.506996e-04
369.0
TRAV17*01
TRAJ27*01
CATDANADKLTF
TRBV19*01
TRBJ2-4*01
CASGQGGQNTQYF
6.678140e-04
4
3
2
global
269
48
6.493992e-01
1
1.588676e-04
389.0
TRAV17*01
TRAJ27*01
CATDTNADKLTF
TRBV19*01
TRBJ2-4*01
CASGQGGQNTQYF
8.869396e-04
4
3
2
Omitted 4 lines
tcr_clumping_logos
This figure summarizes the results of a CoNGA analysis that produces
scores (TCR clumping) and clusters. At the top are six
2D UMAP projections of clonotypes in the dataset based on GEX similarity
(top left three panels) and TCR similarity (top right three panels),
colored from left to right by GEX cluster assignment;
TCR clumping score; joint GEX:TCR cluster assignment for
clonotypes with significant TCR clumping scores,
using a bicolored disk whose left half indicates GEX cluster and whose right
half indicates TCR cluster; TCR cluster; TCR clumping; GEX:TCR cluster
assignments for TCR clumping hits, as in the third panel.
Below are two rows of GEX landscape plots colored by (first row, left)
expression of selected marker genes, (second row, left) Z-score normalized and
GEX-neighborhood averaged expression of the same marker genes, and
(both rows, right) TCR sequence features (see CoNGA manuscript Table S3 for
TCR feature descriptions).
GEX and TCR sequence features of TCR clumping hits in clusters with
3 or more hits are summarized by a series
of logo-style visualizations, from left to right:
differentially expressed genes (DEGs); TCR sequence logos showing the V and
J gene usage and CDR3 sequences for the TCR alpha and beta chains; biased
TCR sequence scores, with red indicating elevated scores and blue indicating
decreased scores relative to the rest of the dataset (see CoNGA manuscript
Table S3 for score definitions); GEX 'logos' for each cluster
consisting of a panel of marker genes shown with red disks colored by
mean expression and sized according to the fraction of cells expressing
the gene (gene names are given above).
DEG and TCRseq sequence logos are scaled
by the adjusted P value of the associations, with full logo height requiring
a top adjusted P value below 10-6. DEGs with fold-change less than 2 are shown
in gray. Each cluster is indicated by a bicolored disk colored according to
GEX cluster (left half) and TCR cluster (right half). The two numbers above
each disk show the number of hits within the cluster (on the left) and
the total number of cells in those clonotypes (on the right). The dendrogram
at the left shows similarity relationships among the clusters based on
connections in the GEX and TCR neighbor graphs.
The choice of which marker genes to use for the GEX umap panels and for the
cluster GEX logos can be configured using run_conga.py command line flags
or arguments to the conga.plotting.make_logo_plots function.
Image source: Cobain_GIC_Final2_tcr_clumping_logos.png
tcr_db_match
This table stores significant matches between
TCRs in adata and TCRs in the file /scratch.global/ben_testing/conga/conga/data/new_paired_tcr_db_for_matching_nr.tsv
P values of matches are assigned by turning the raw TCRdist
score into a P value based on a model of the V(D)J rearrangement
process, so matches between TCRs that are very far from germline
(for example) are assigned a higher significance.
Columns:
tcrdist: TCRdist distance between the two TCRs (adata query and db hit)
pvalue_adj: raw P value of the match * num query TCRs * num db TCRs
fdr_value: Benjamini-Hochberg FDR value for match
clone_index: index within adata of the query TCR clonotype
db_index: index of the hit in the database being matched
va,ja,cdr3a,vb,jb,cdr3b
db_XXX: where XXX is a field in the literature database
tcr_graph_vs_gex_features
This table has results from a graph-vs-features analysis in which we
look for genes that are differentially expressed (elevated) in specific
neighborhoods of the TCR neighbor graph. Differential expression is
assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
gene.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
log2enr = log2 fold change of gene in neighborhood (will be positive)
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the gene
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
ttest_pvalue_adj
mwu_pvalue_adj
log2enr
gex_cluster
tcr_cluster
feature
mean_fg
mean_bg
num_fg
clone_index
mait_fraction
nbr_frac
graph_type
feature_type
2.892767e-19
3.397924e-74
5.760394
2
6
ENSMMUG00000043894
2.432636
0.175342
71
-1
0.0
0.0
tcr_cluster
gex
1.089014e-08
1.064123e-60
5.712788
0
10
ENSMMUG00000061119
1.753271
0.087108
36
-1
0.0
0.0
tcr_cluster
gex
1.364521e-10
8.285322e-47
4.522135
2
6
ENSMMUG00000043894
1.703045
0.178513
103
415
0.0
0.1
tcr_nbr
gex
7.391521e-09
5.327159e-41
4.325845
2
6
ENSMMUG00000043894
1.631611
0.186519
103
107
0.0
0.1
tcr_nbr
gex
8.861353e-09
2.750179e-39
4.315207
2
6
ENSMMUG00000043894
1.627734
0.186954
103
626
0.0
0.1
tcr_nbr
gex
1.066617e-08
6.673187e-39
4.273937
2
6
ENSMMUG00000043894
1.612688
0.188640
103
248
0.0
0.1
tcr_nbr
gex
3.683860e-01
6.759251e-36
6.061486
0
1
ENSMMUG00000060662
0.797168
0.018091
103
924
0.0
0.1
tcr_nbr
gex
5.602167e-08
2.577416e-35
4.175139
2
6
ENSMMUG00000043894
1.576652
0.192679
103
301
0.0
0.1
tcr_nbr
gex
2.262062e-07
6.309623e-35
4.071092
2
6
ENSMMUG00000043894
1.538696
0.196933
103
59
0.0
0.1
tcr_nbr
gex
1.756006e-07
1.146475e-34
4.027714
2
6
ENSMMUG00000043894
1.522876
0.198706
103
178
0.0
0.1
tcr_nbr
gex
1.151267e-07
1.506979e-34
4.235354
2
6
ENSMMUG00000043894
1.598617
0.190217
103
785
0.0
0.1
tcr_nbr
gex
1.537118e-07
8.457291e-34
4.123988
2
6
ENSMMUG00000043894
1.557992
0.194770
103
482
0.0
0.1
tcr_nbr
gex
3.188034e-07
4.091844e-33
4.003964
2
6
ENSMMUG00000043894
1.514216
0.199677
103
479
0.0
0.1
tcr_nbr
gex
3.532596e-07
4.468555e-33
4.001371
2
6
ENSMMUG00000043894
1.513271
0.199783
103
418
0.0
0.1
tcr_nbr
gex
3.167149e-07
5.078867e-33
4.003478
2
6
ENSMMUG00000043894
1.514039
0.199697
103
432
0.0
0.1
tcr_nbr
gex
6.089620e-07
7.975956e-33
3.970755
2
6
ENSMMUG00000043894
1.502111
0.201033
103
946
0.0
0.1
tcr_nbr
gex
5.613666e-07
1.155395e-32
3.947235
2
6
ENSMMUG00000043894
1.493540
0.201994
103
101
0.0
0.1
tcr_nbr
gex
8.191486e-01
1.204519e-32
5.719125
0
1
ENSMMUG00000060662
0.765785
0.021609
103
923
0.0
0.1
tcr_nbr
gex
3.365246e-07
2.064042e-32
4.113990
2
6
ENSMMUG00000043894
1.554344
0.195179
103
758
0.0
0.1
tcr_nbr
gex
3.440516e-06
1.180600e-30
3.804360
2
6
ENSMMUG00000043894
1.441542
0.207822
103
994
0.0
0.1
tcr_nbr
gex
1.419424e+00
2.054940e-30
4.640636
2
4
ENSMMUG00000052673
0.505643
0.026039
103
544
0.0
0.1
tcr_nbr
gex
1.711255e+00
2.961670e-30
4.503088
2
4
ENSMMUG00000052673
0.491586
0.027614
103
534
0.0
0.1
tcr_nbr
gex
2.219197e-06
8.983608e-30
3.919719
2
6
ENSMMUG00000043894
1.483516
0.203118
103
158
0.0
0.1
tcr_nbr
gex
1.759829e+00
1.224345e-29
5.504371
0
1
ENSMMUG00000060662
0.744081
0.024041
103
933
0.0
0.1
tcr_nbr
gex
2.081256e+00
1.690525e-29
5.374644
0
1
ENSMMUG00000060662
0.730228
0.025594
103
928
0.0
0.1
tcr_nbr
gex
3.165294e+00
1.985984e-29
5.238837
0
1
ENSMMUG00000060662
0.715144
0.027284
103
942
0.0
0.1
tcr_nbr
gex
1.700937e-03
3.580677e-29
4.386767
2
2
ENSMMUG00000062085
1.077587
0.088580
103
504
0.0
0.1
tcr_nbr
gex
3.839802e+00
3.827329e-29
5.002207
0
1
ENSMMUG00000060662
0.687489
0.030384
103
953
0.0
0.1
tcr_nbr
gex
2.944461e-06
4.075794e-29
3.822363
2
6
ENSMMUG00000043894
1.448086
0.207088
103
511
0.0
0.1
tcr_nbr
gex
1.894907e-01
5.332926e-29
4.193284
0
1
ENSMMUG00000057062
0.456475
0.031133
103
882
0.0
0.1
tcr_nbr
gex
2.380103e-06
1.261190e-28
3.950724
2
6
ENSMMUG00000043894
1.494811
0.201852
103
241
0.0
0.1
tcr_nbr
gex
6.128023e-02
2.962608e-28
4.347653
2
4
ENSMMUG00000052673
0.483071
0.030048
100
-1
0.0
0.0
tcr_cluster
gex
3.388499e-06
3.743188e-28
3.867162
2
6
ENSMMUG00000043894
1.464382
0.205262
103
959
0.0
0.1
tcr_nbr
gex
3.067582e+00
1.169482e-27
4.376205
2
4
ENSMMUG00000052673
0.478284
0.029105
103
564
0.0
0.1
tcr_nbr
gex
3.784933e+00
1.452422e-27
4.398505
2
4
ENSMMUG00000052673
0.480644
0.028841
103
552
0.0
0.1
tcr_nbr
gex
3.905234e+00
1.585636e-27
4.358971
2
4
ENSMMUG00000052673
0.476454
0.029310
103
556
0.0
0.1
tcr_nbr
gex
3.802922e+00
1.623164e-27
4.365042
2
4
ENSMMUG00000052673
0.477099
0.029238
103
548
0.0
0.1
tcr_nbr
gex
4.367138e+00
1.835152e-27
4.304220
2
4
ENSMMUG00000052673
0.470606
0.029966
103
533
0.0
0.1
tcr_nbr
gex
4.236369e+00
2.186521e-27
4.200551
2
4
ENSMMUG00000052673
0.459394
0.031222
103
563
0.0
0.1
tcr_nbr
gex
1.182252e-05
4.440368e-27
3.855867
2
6
ENSMMUG00000043894
1.460272
0.205723
103
46
0.0
0.1
tcr_nbr
gex
7.825501e-06
4.814517e-27
3.864251
2
6
ENSMMUG00000043894
1.463323
0.205381
103
963
0.0
0.1
tcr_nbr
gex
8.149115e-06
6.506373e-27
3.865820
2
6
ENSMMUG00000043894
1.463894
0.205317
103
949
0.0
0.1
tcr_nbr
gex
8.783328e-06
8.852021e-27
3.831511
2
6
ENSMMUG00000043894
1.451413
0.206716
103
819
0.0
0.1
tcr_nbr
gex
1.614262e-05
9.629497e-27
3.799316
2
6
ENSMMUG00000043894
1.439709
0.208027
103
185
0.0
0.1
tcr_nbr
gex
5.078142e+00
1.343536e-26
5.122255
0
1
ENSMMUG00000060662
0.701731
0.028788
103
944
0.0
0.1
tcr_nbr
gex
8.227295e+00
1.876362e-26
4.931847
0
1
ENSMMUG00000060662
0.678946
0.031341
103
941
0.0
0.1
tcr_nbr
gex
2.051007e-05
4.690201e-26
3.660968
2
6
ENSMMUG00000043894
1.389521
0.213652
103
725
0.0
0.1
tcr_nbr
gex
5.344732e+00
3.043984e-25
4.389552
2
4
ENSMMUG00000052673
0.479697
0.028947
103
530
0.0
0.1
tcr_nbr
gex
5.919114e+00
3.446155e-25
4.359832
2
4
ENSMMUG00000052673
0.476545
0.029300
103
528
0.0
0.1
tcr_nbr
gex
5.919114e+00
3.446155e-25
4.359832
2
4
ENSMMUG00000052673
0.476545
0.029300
103
529
0.0
0.1
tcr_nbr
gex
Omitted 238 lines
tcr_graph_vs_gex_features_plot
This plot summarizes the results of a graph
versus features analysis by labeling the clonotypes at the center of
each biased neighborhood with the name of the feature biased in that
neighborhood. The feature names are drawn in colored boxes whose
color is determined by the strength and direction of the feature score bias
(from bright red for features that are strongly elevated to bright blue
for features that are strongly decreased in the corresponding neighborhoods,
relative to the rest of the dataset).
At most one feature (the top scoring) is shown for each clonotype
(ie, neighborhood). The UMAP xy coordinates for this plot are
stored in adata.obsm['X_tcr_2d']. The score used for ranking correlations
is 'mwu_pvalue_adj'. The threshold score for displaying a feature is
1.0. The feature column is 'feature'. Since
we also run graph-vs-features using "neighbor" graphs that are defined
by clusters, ie where each clonotype is connected to all the other
clonotypes in the same cluster, some biased features may be associated with
a cluster rather than a specific clonotype. Those features are labeled with
a '*' at the end and shown near the centroid of the clonotypes belonging
to that cluster.
Image source: Cobain_GIC_Final2_tcr_graph_vs_gex_features_plot.png
tcr_graph_vs_gex_features_panels
Graph-versus-feature analysis was used to identify
a set of GEX features that showed biased distributions
in TCR neighborhoods. This plot shows the distribution of the
top-scoring GEX features on the TCR
UMAP 2D landscape. The features are ranked by 'mwu_pvalue_adj' ie
Mann-Whitney-Wilcoxon adjusted P value (raw P value * number of comparisons).
At most 3 features from clonotype neighbhorhoods
in each (GEX,TCR) cluster pair are shown. The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Points are plotted in order of increasing feature score.
Image source: Cobain_GIC_Final2_tcr_graph_vs_gex_features_panels.png
tcr_genes_vs_gex_features
This table has results from a graph-vs-features analysis in which we
look for genes that are differentially expressed (elevated) in specific
neighborhoods of the TCR neighbor graph. Differential expression is
assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
gene.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
log2enr = log2 fold change of gene in neighborhood (will be positive)
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the gene
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
In this analysis the TCR graph is defined by
connecting all clonotypes that have the same VA/JA/VB/JB-gene segment
(it's run four times, once with each gene segment type)
ttest_pvalue_adj
mwu_pvalue_adj
log2enr
gex_cluster
tcr_cluster
feature
mean_fg
mean_bg
num_fg
clone_index
mait_fraction
gene_segment
graph_type
feature_type
7.680095e+00
1.487624e-218
NaN
6
5
ENSMMUG00000048246
3.234783
-1.873645e-09
6
-1
0.000000
TRBV6-8
tcr_genes
gex
8.028887e-14
2.917151e-168
10.269545
0
1
ENSMMUG00000060662
2.728752
1.152940e-02
32
-1
0.000000
TRAV8-7
tcr_genes
gex
2.437364e-01
1.368213e-163
12.038369
0
1
ENSMMUG00000059234
2.615368
3.008084e-03
9
-1
0.000000
TRBV25-1
tcr_genes
gex
5.133844e-04
3.438427e-155
9.972508
6
1
ENSMMUG00000062897
2.403146
9.961364e-03
15
-1
0.000000
TRBV11-2
tcr_genes
gex
1.048790e-13
1.937740e-144
9.777905
0
10
ENSMMUG00000063185
2.975444
2.096385e-02
31
-1
0.000000
TRBV4-2
tcr_genes
gex
6.739993e-26
3.745618e-142
8.207480
0
3
ENSMMUG00000062085
2.643389
4.323633e-02
57
-1
0.000000
TRBV4-3
tcr_genes
gex
2.737426e-13
2.783030e-130
9.048454
0
1
ENSMMUG00000062211
3.003197
3.552807e-02
33
-1
0.000000
TRBV12-2
tcr_genes
gex
2.132582e-04
1.006423e-124
8.088103
2
4
ENSMMUG00000056431
1.916044
2.106862e-02
20
-1
0.000000
TRAV35
tcr_genes
gex
4.244478e-06
1.347413e-106
6.957203
2
4
ENSMMUG00000052673
1.189393
1.822269e-02
49
-1
0.000000
TRAV27
tcr_genes
gex
3.387262e-05
2.640779e-105
8.074643
1
1
ENSMMUG00000056910
1.911052
2.114114e-02
17
-1
0.000000
TRAV16
tcr_genes
gex
2.744935e-40
1.802070e-101
6.715584
2
6
ENSMMUG00000043894
2.955590
1.598175e-01
63
-1
0.000000
TRBV20-1
tcr_genes
gex
2.658563e-05
6.566327e-98
7.110737
0
2
ENSMMUG00000054409
1.627660
2.917654e-02
30
-1
0.000000
TRAV6
tcr_genes
gex
4.502685e-08
2.741429e-91
7.830931
0
0
ENSMMUG00000065017
2.286982
3.811179e-02
23
-1
0.000000
TRAV12-1
tcr_genes
gex
3.779473e-03
1.091229e-84
7.699737
0
4
ENSMMUG00000059325
1.992804
3.002155e-02
20
-1
0.000000
TRAV25
tcr_genes
gex
9.277174e-18
1.995422e-84
6.285125
0
10
ENSMMUG00000061119
1.994806
7.828967e-02
36
-1
0.000000
TRAV18
tcr_genes
gex
1.553028e-04
2.356232e-74
5.894151
0
1
ENSMMUG00000061081
0.880054
2.344868e-02
48
-1
0.000000
TRAV8-2
tcr_genes
gex
2.053014e-05
3.280283e-72
5.772890
0
1
ENSMMUG00000057062
0.943915
2.830943e-02
51
-1
0.000000
TRAV8-3
tcr_genes
gex
5.678434e-61
9.028388e-66
5.071222
0
3
ENSMMUG00000056515
2.987117
4.447157e-01
89
-1
0.000000
TRBV6-3
tcr_genes
gex
4.119979e-17
3.785737e-61
7.109418
0
0
ENSMMUG00000051385
3.076480
1.395675e-01
29
-1
0.000000
TRBV7-4
tcr_genes
gex
5.181498e-04
8.604369e-46
6.726140
2
2
ENSMMUG00000062974
2.156282
6.967033e-02
13
-1
0.000000
TRAV13-2
tcr_genes
gex
1.173425e-15
5.751559e-44
5.448288
1
5
ENSMMUG00000043894
2.628155
2.579457e-01
32
-1
0.000000
TRBV19
tcr_genes
gex
7.460720e-01
2.190617e-32
6.246444
0
5
ENSMMUG00000062211
2.302868
1.120602e-01
9
-1
0.000000
TRBV12-3
tcr_genes
gex
3.877101e-03
1.211601e-27
2.900490
0
3
ENSMMUG00000061119
0.593705
1.030727e-01
89
-1
0.000000
TRAV19
tcr_genes
gex
2.189019e-25
1.551478e-27
4.503213
0
1
ENSMMUG00000056515
2.908419
5.676314e-01
43
-1
0.100000
TRBV10-2
tcr_genes
gex
3.244874e-15
8.271428e-23
4.200101
0
1
ENSMMUG00000056515
2.740876
5.816071e-01
40
-1
0.000000
TRBV6-2
tcr_genes
gex
6.150524e-04
1.308301e-21
6.151809
0
1
ENSMMUG00000051385
2.778609
1.925398e-01
12
-1
0.000000
TRBV7-6
tcr_genes
gex
1.683511e+00
1.945236e-19
4.861590
2
5
ENSMMUG00000051385
1.998051
1.982498e-01
14
-1
0.000000
TRBV5-6
tcr_genes
gex
1.120149e-01
2.156665e-15
4.792311
1
1
ENSMMUG00000043894
2.362086
2.978226e-01
17
-1
0.000000
TRBV21-1
tcr_genes
gex
4.998835e-01
1.576433e-12
3.767046
4
8
KLRB1
1.498821
2.274150e-01
32
-1
1.000000
TRAV1-2
tcr_genes
gex
1.900278e-01
8.629206e-06
2.087580
0
3
ENSMMUG00000056515
1.546471
6.255701e-01
45
-1
0.000000
TRBV9
tcr_genes
gex
6.111556e-01
4.133253e-04
2.348992
0
4
ENSMMUG00000056515
1.711141
6.366813e-01
28
-1
0.000000
TRBV10-1
tcr_genes
gex
5.625136e+00
1.952271e-02
2.281442
4
8
IL7R
1.939922
8.000069e-01
32
-1
1.000000
TRAV1-2
tcr_genes
gex
6.899273e+00
3.391942e-02
1.825299
3
5
PPDPF
1.242306
5.277901e-01
29
-1
0.000000
TRBV7-4
tcr_genes
gex
3.581038e-01
2.756213e-01
0.929537
0
1
TIGAR
1.490060
1.031299e+00
97
-1
0.041667
TRBJ1-2
tcr_genes
gex
2.382486e-03
4.042441e-01
0.416653
1
4
RPL35A
3.630398
3.350432e+00
49
-1
0.000000
TRAV27
tcr_genes
gex
5.202479e-01
1.337438e+00
0.426685
1
6
RPL8
3.215522
2.933484e+00
63
-1
0.000000
TRBV20-1
tcr_genes
gex
6.754571e-01
4.552175e+00
2.381771
2
2
ENSMMUG00000006206
1.457456
4.899458e-01
8
-1
0.000000
TRAJ3
tcr_genes
gex
tcr_genes_vs_gex_features_panels
Graph-versus-feature analysis was used to identify
a set of GEX features that showed biased distributions
in TCR neighborhoods. This plot shows the distribution of the
top-scoring GEX features on the TCR
UMAP 2D landscape. The features are ranked by 'mwu_pvalue_adj' ie
Mann-Whitney-Wilcoxon adjusted P value (raw P value * number of comparisons).
At most 3 features from clonotype neighbhorhoods
in each (GEX,TCR) cluster pair are shown. The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Points are plotted in order of increasing feature score.
Image source: Cobain_GIC_Final2_tcr_genes_vs_gex_features_panels.png
gex_graph_vs_tcr_features
This table has results from a graph-vs-features analysis in which we
look at the distribution of a set of TCR-defined features over the GEX
neighbor graph. We look for neighborhoods in the graph that have biased
score distributions, as assessed by a ttest first, for speed, and then
by a mannwhitneyu test for nbrhood/score combinations whose ttest P-value
passes an initial threshold (default is 10* the pvalue threshold).
Each row of the table represents a single significant association, in other
words a neighborhood (defined by the central clonotype index) and a
tcr feature.
The columns are as follows:
ttest_pvalue_adj= ttest_pvalue * number of comparisons
ttest_stat= ttest statistic (sign indicates where feature is up or down)
mwu_pvalue_adj= mannwhitney-U P-value * number of comparisons
gex_cluster= the consensus GEX cluster of the clonotypes w/ biased scores
tcr_cluster= the consensus TCR cluster of the clonotypes w/ biased scores
num_fg= the number of clonotypes in the neighborhood (including center)
mean_fg= the mean value of the feature in the neighborhood
mean_bg= the mean value of the feature outside the neighborhood
feature= the name of the TCR score
mait_fraction= the fraction of the skewed clonotypes that have an invariant
TCR
clone_index= the index in the anndata dataset of the clonotype that is the
center of the neighborhood.
ttest_pvalue_adj
ttest_stat
mwu_pvalue_adj
gex_cluster
tcr_cluster
num_fg
mean_fg
mean_bg
feature
mait_fraction
clone_index
nbr_frac
graph_type
feature_type
0.002003
5.266544
8.875816e-54
4
8
69
0.289855
0.002099
mait
1.000000
-1
0.00
gex_cluster
tcr
0.000840
5.486600
1.298149e-42
4
8
69
0.318841
0.010493
TRAV1-2
0.882353
-1
0.00
gex_cluster
tcr
0.547702
4.922232
7.170575e-32
4
8
103
0.194175
0.002176
mait
0.800000
24
0.10
gex_nbr
tcr
0.388360
5.001786
7.130560e-24
4
8
103
0.213592
0.010881
TRAV1-2
0.800000
24
0.10
gex_nbr
tcr
5.272281
4.353944
6.279203e-21
4
8
103
0.165049
0.005441
mait
0.680000
25
0.10
gex_nbr
tcr
5.272281
4.353944
6.279203e-21
4
8
103
0.165049
0.005441
mait
0.680000
41
0.10
gex_nbr
tcr
0.064964
4.327631
5.109696e-19
4
8
69
0.246377
0.020986
TRBJ2-6
0.705882
-1
0.00
gex_cluster
tcr
3.834780
4.433647
8.530963e-16
4
8
103
0.184466
0.014146
TRAV1-2
0.680000
41
0.10
gex_nbr
tcr
3.206622
4.478261
2.470043e-14
4
8
103
0.194175
0.018498
TRBJ2-6
0.480000
24
0.10
gex_nbr
tcr
8.110873
4.238550
2.078654e-13
4
8
103
0.174757
0.015234
TRAV1-2
0.640000
23
0.10
gex_nbr
tcr
0.059479
4.348959
2.510116e-13
4
8
69
0.275362
0.039874
TRAJ33
1.000000
-1
0.00
gex_cluster
tcr
5.827015
2.882367
1.035680e-03
3
3
158
0.069620
0.010417
TRAV17
0.000000
-1
0.00
gex_cluster
tcr
0.000862
5.026611
2.711672e-03
0
3
297
0.210607
0.055467
cd8
0.013514
-1
0.00
gex_cluster
tcr
0.003944
5.010718
7.681031e-03
4
1
69
78.420290
65.929696
alphadist
0.058824
-1
0.00
gex_cluster
tcr
0.064001
-4.129941
5.010006e-02
2
1
183
-0.033109
0.129706
cd8
0.000000
-1
0.00
gex_cluster
tcr
0.003420
-4.786657
9.405589e-02
1
6
184
-0.031455
0.129537
cd8
0.000000
-1
0.00
gex_cluster
tcr
0.375490
-3.802146
1.662729e-01
4
8
69
-0.119680
0.436249
af5
0.764706
-1
0.00
gex_cluster
tcr
0.000731
-5.037161
1.812127e-01
0
5
297
0.016835
0.080000
TRBV20-1
0.000000
-1
0.00
gex_cluster
tcr
0.277927
-3.889917
2.232103e-01
4
8
69
-0.695780
0.037686
af3
0.647059
-1
0.00
gex_cluster
tcr
0.311807
-3.862978
3.091960e-01
4
8
69
-0.246574
0.151507
kf7
0.705882
-1
0.00
gex_cluster
tcr
0.008690
-5.760626
3.366695e-01
1
6
103
-0.113480
0.124540
cd8
0.000000
593
0.10
gex_nbr
tcr
6.534299
2.835147
3.637232e-01
2
6
183
0.120219
0.048868
TRBV20-1
0.000000
-1
0.00
gex_cluster
tcr
0.285774
-5.022732
3.672394e-01
2
6
103
-0.120508
0.125328
cd8
0.000000
163
0.10
gex_nbr
tcr
0.616313
4.835466
5.733172e-01
0
1
103
0.299643
0.078238
cd8
0.000000
20
0.10
gex_nbr
tcr
9.197958
-6.563406
5.917695e-01
4
8
11
-0.939361
0.136207
kf7
1.000000
27
0.01
gex_nbr
tcr
0.231033
-5.069156
6.242221e-01
2
6
103
-0.118154
0.125064
cd8
0.000000
1010
0.10
gex_nbr
tcr
3.020025
3.064586
7.254659e-01
0
3
297
0.134680
0.067586
TRAV19
0.000000
-1
0.00
gex_cluster
tcr
0.145216
-5.166565
8.317266e-01
2
6
103
-0.109760
0.124123
cd8
0.000000
545
0.10
gex_nbr
tcr
0.856814
-3.563955
5.661843e+00
4
8
69
0.543890
0.582572
nndists_tcr
0.941176
-1
0.00
gex_cluster
tcr
0.601287
-4.829535
7.050044e+00
1
6
103
-0.081544
0.120961
cd8
0.000000
432
0.10
gex_nbr
tcr
0.276291
-5.017002
7.982202e+00
1
6
103
-0.099078
0.122926
cd8
0.000000
129
0.10
gex_nbr
tcr
0.272385
-5.009599
8.364139e+00
1
0
103
-0.085437
0.121397
cd8
0.000000
680
0.10
gex_nbr
tcr
gex_graph_vs_tcr_features_plot
This plot summarizes the results of a graph
versus features analysis by labeling the clonotypes at the center of
each biased neighborhood with the name of the feature biased in that
neighborhood. The feature names are drawn in colored boxes whose
color is determined by the strength and direction of the feature score bias
(from bright red for features that are strongly elevated to bright blue
for features that are strongly decreased in the corresponding neighborhoods,
relative to the rest of the dataset).
At most one feature (the top scoring) is shown for each clonotype
(ie, neighborhood). The UMAP xy coordinates for this plot are
stored in adata.obsm['X_gex_2d']. The score used for ranking correlations
is 'mwu_pvalue_adj'. The threshold score for displaying a feature is
1.0. The feature column is 'feature'. Since
we also run graph-vs-features using "neighbor" graphs that are defined
by clusters, ie where each clonotype is connected to all the other
clonotypes in the same cluster, some biased features may be associated with
a cluster rather than a specific clonotype. Those features are labeled with
a '*' at the end and shown near the centroid of the clonotypes belonging
to that cluster.
Image source: Cobain_GIC_Final2_gex_graph_vs_tcr_features_plot.png
gex_graph_vs_tcr_features_panels
Graph-versus-feature analysis was used to identify
a set of TCR features that showed biased distributions
in GEX neighborhoods. This plot shows the distribution of the
top-scoring TCR features on the GEX
UMAP 2D landscape. The features are ranked by 'mwu_pvalue_adj' ie
Mann-Whitney-Wilcoxon adjusted P value (raw P value * number of comparisons).
At most 3 features from clonotype neighbhorhoods
in each (GEX,TCR) cluster pair are shown. The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Points are plotted in order of increasing feature score.
Image source: Cobain_GIC_Final2_gex_graph_vs_tcr_features_panels.png
graph_vs_features_gex_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
GEX landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_gex' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are GEX clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=102 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie GEX features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the GEX features).
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
TCR landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_tcr' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are TCR clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=102 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie TCR features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the TCR features).
Summary figure for the graph-vs-graph and
graph-vs-features analyses.
Image source: Cobain_GIC_Final2_graph_vs_summary.png
gex_clusters_tcrdist_trees
These are TCRdist hierarchical clustering trees
for the GEX clusters (cluster assignments stored in
adata.obs['clusters_gex']). The trees are colored by CoNGA score
with a color score range of 1.02e+01 (blue) to 1.02e-08 (red).
For coloring, CoNGA scores are log-transformed, negated, and square-rooted
(with an offset in there, too, roughly speaking).
Image source: Cobain_GIC_Final2_gex_clusters_tcrdist_trees.png
conga_threshold_tcrdist_tree
This is a TCRdist hierarchical clustering tree
for the clonotypes with CoNGA score less than 10.0.
The tree is colored by CoNGA score
with a color score range of 1.00e+01 (blue) to 1.00e-08 (red).
For coloring, CoNGA scores are log-transformed, negated, and square-rooted
(with an offset in there, too, roughly speaking).
Image source: Cobain_GIC_Final2_conga_threshold_tcrdist_tree.png
hotspot_features
Find GEX (TCR) features that show a biased
distribution across the TCR (GEX) neighbor graph,
using a simplified version of the Hotspot method
from the Yosef lab.
DeTomaso, D., & Yosef, N. (2021).
"Hotspot identifies informative gene modules across modalities
of single-cell genomics."
Cell Systems, 12(5), 446–456.e9.
PMID:33951459
Columns:
Z: HotSpot Z statistic
pvalue_adj: Raw P value times the number of tests (crude Bonferroni
correction)
nbr_frac: The K NN nbr fraction used for the neighbor graph construction
(nbr_frac = 0.1 means K=0.1*num_clonotypes neighbors)
Z
pvalue_adj
feature
feature_type
nbr_frac
63.643690
0.000000e+00
ENSMMUG00000056515
gex
0.10
59.411769
0.000000e+00
ENSMMUG00000043894
gex
0.10
41.269847
0.000000e+00
ENSMMUG00000061119
gex
0.10
40.066080
0.000000e+00
ENSMMUG00000062085
gex
0.10
39.953858
0.000000e+00
ENSMMUG00000060662
gex
0.10
39.472488
0.000000e+00
ENSMMUG00000060662
gex
0.01
38.206218
0.000000e+00
ENSMMUG00000052673
gex
0.10
35.967220
1.946855e-279
ENSMMUG00000043894
gex
0.01
35.168258
4.370481e-267
ENSMMUG00000056515
gex
0.01
33.336175
8.259764e-240
ENSMMUG00000057062
gex
0.10
29.458605
6.982233e-187
ENSMMUG00000061119
gex
0.01
26.095667
2.918464e-146
ENSMMUG00000061081
gex
0.10
25.196685
3.113142e-136
ENSMMUG00000062085
gex
0.01
25.093568
4.178786e-135
ENSMMUG00000062211
gex
0.10
24.363803
3.601598e-129
mait
tcr
0.10
24.372706
2.381113e-127
ENSMMUG00000057062
gex
0.01
23.428392
1.569420e-117
ENSMMUG00000054409
gex
0.10
22.289899
4.028425e-108
mait
tcr
0.01
21.784105
2.346674e-101
ENSMMUG00000052673
gex
0.01
21.616693
8.944171e-100
ENSMMUG00000065017
gex
0.10
20.803983
2.847160e-92
ENSMMUG00000054409
gex
0.01
20.422579
7.530645e-89
CEBPD
gex
0.01
19.385046
7.377658e-80
gex_cluster4
gex
0.01
18.691667
4.137002e-74
ENSMMUG00000056431
gex
0.10
17.915819
6.344050e-68
ENSMMUG00000065017
gex
0.01
17.755709
1.112891e-66
ENSMMUG00000056431
gex
0.01
17.437876
3.042184e-64
ENSMMUG00000061081
gex
0.01
16.447369
7.620416e-59
TRAV1-2
tcr
0.10
16.591287
5.759498e-58
ENSMMUG00000063185
gex
0.10
15.681633
1.757348e-53
TRAV1-2
tcr
0.01
15.085948
1.432285e-47
ENSMMUG00000062211
gex
0.01
14.305926
1.436347e-42
ENSMMUG00000051385
gex
0.10
13.955132
2.092637e-40
ENSMMUG00000059325
gex
0.10
13.575538
4.866011e-40
cd8
tcr
0.10
13.766224
2.908768e-39
CEBPD
gex
0.10
13.386066
5.213968e-37
gex_cluster4
gex
0.10
12.648722
8.127933e-33
ENSMMUG00000003532
gex
0.10
12.609744
1.333800e-32
ARHGAP8
gex
0.01
11.461007
1.480295e-26
ENSMMUG00000063185
gex
0.01
11.332531
6.472525e-26
ENSMMUG00000059325
gex
0.01
10.567272
3.020817e-22
gex_cluster0
gex
0.10
10.134396
2.778910e-20
ENSMMUG00000051385
gex
0.01
9.463995
2.578652e-19
TRBJ2-6
tcr
0.10
9.711782
1.919955e-18
KLRB1
gex
0.01
9.238144
2.182051e-18
tcr_cluster8
tcr
0.10
8.694954
3.018653e-16
tcr_cluster6
tcr
0.10
8.612584
6.214564e-16
tcr_cluster8
tcr
0.01
8.903537
3.866700e-15
ENSMMUG00000056910
gex
0.10
8.841629
6.742919e-15
KLRG1
gex
0.01
8.226785
1.673060e-14
TRBV20-1
tcr
0.10
Omitted 79 lines
hotspot_gex_umap
HotSpot analysis (Nir Yosef lab, PMID: 33951459)
was used to identify a set of GEX (TCR) features that showed biased
distributions in TCR (GEX) space. This plot shows the distribution of the
top-scoring HotSpot features on the GEX
UMAP 2D landscape. The features are ranked by adjusted P value
(raw P value * number of comparisons). The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Features are filtered based on correlation coefficient to reduce
redundancy: if a feature has a correlation of >= 0.9
(the max_feature_correlation argument to conga.plotting.plot_hotspot_umap)
to a previously plotted feature, that feature is skipped.
Points are plotted in order of increasing feature score
Image source: Cobain_GIC_Final2_hotspot_combo_features_0.100_nbrs_gex_plot_umap_nbr_avg.png
hotspot_gex_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
GEX landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_gex' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are GEX clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=102 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie GEX features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the GEX features).
HotSpot analysis (Nir Yosef lab, PMID: 33951459)
was used to identify a set of GEX (TCR) features that showed biased
distributions in TCR (GEX) space. This plot shows the distribution of the
top-scoring HotSpot features on the TCR
UMAP 2D landscape. The features are ranked by adjusted P value
(raw P value * number of comparisons). The raw scores for each feature
are averaged over the K nearest neighbors (K is indicated in the lower
right corner of each panel) for each clonotype. The min and max
nbr-averaged scores are shown in the upper corners of each panel.
Features are filtered based on correlation coefficient to reduce
redundancy: if a feature has a correlation of >= 0.9
(the max_feature_correlation argument to conga.plotting.plot_hotspot_umap)
to a previously plotted feature, that feature is skipped.
Points are plotted in order of increasing feature score
Image source: Cobain_GIC_Final2_hotspot_combo_features_0.100_nbrs_tcr_plot_umap_nbr_avg.png
hotspot_tcr_clustermap
This plot shows the distribution of significant
features from graph-vs-features or HotSpot analysis plotted across the
TCR landscape. Rows are features and columns are
individual clonotypes. Columns are ordered by hierarchical clustering
(if a dendrogram is present above the heatmap) or by a 1D UMAP projection
(used for very large datasets or if 'X_pca_tcr' is not present in
adata.obsm_keys()). Rows are ordered by hierarchical clustering with
a correlation metric.
The row colors to the left of the heatmap show the feature type
(blue=TCR, orange=GEX). The row colors to the left of those
indicate the strength of the graph-vs-feature correlation
(also included in the feature labels to the right of the heatmap;
keep in mind that highly significant P values for some features may shift
the colorscale so everything else looks dark blue).
The column colors above the heatmap are TCR clusters
(and TCR V/J genes if plotting against the TCR landscape). The text
above the column colors provides more info.
Feature scores are Z-score normalized and then averaged over the
K=102 nearest neighbors (0 means no nbr-averaging).
The 'coolwarm' colormap is centered at Z=0.
Since features of the same type (GEX or TCR) as the landscape and
neighbor graph (ie TCR features) are more highly
correlated over graph neighborhoods, their neighbor-averaged scores
will show more extreme variation. For this reason, the nbr-averaged
scores for these features from the same modality as the landscape
itself are downscaled by a factor of
rescale_factor_for_self_features=0.33.
The colormap in the top left is for the Z-score normalized,
neighbor-averaged scores (multiply by 3.03
to get the color scores for the TCR features).